A transcription activator-like effector toolbox for genome engineering

Sanjana, Neville E.; Cong, Le; Zhou, Yang; Cunniff, Margaret M; Feng, Guoping; Zhang, Feng

doi:10.1038/nprot.2011.431

Cited by 592 publications

(559 citation statements)

References 60 publications

(100 reference statements)

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“…Just after this manuscript was submitted, a study appeared in which TALE-FPs were used to label repeated sequences in both cultured mouse cells and embryos (25). The applications presented in that important study and the present one are different but complementary.…”

Section: Discussionmentioning

confidence: 99%

Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors

Reyes-Gutierrez

Pederson

2013

Proc. Natl. Acad. Sci. U.S.A.

112

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The authors note that, due to a printer's error, references 41-50 appeared incorrectly. The corrected references follow. The authors note: "Our paper unfortunately missed reference to an earlier suggestion of the T6 structure (43). This work entitled 'A hypothetical dense 3,4-connected carbon net and related B 2 C and CN 2 nets built from 1,4-cyclohexadienoid units' by M. J. Bucknum and R. Hoffmann was published in J Am Chem Soc 116: 11456-11464 (1994), where the electronic structure of a hypothetical 3,4-connected tetragonal allotrope of carbon is discussed. The results in this article are consistent with what we find. The same group had also suggested a metallic carbon structure (44) that was published in J Am Chem Soc 105: 4831-4832 (1983), which we also missed to cite. We thank Prof. Hoffmann for bringing these papers to our attention."The complete references appear below. www.pnas.org/cgi

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Section: Discussionmentioning

confidence: 99%

Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors

Reyes-Gutierrez

Pederson

2013

Proc. Natl. Acad. Sci. U.S.A.

112

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“…TALENs targeting the murine Satb1 locus were designed using the TAL Effector Nucleotide Targeter 36 and assembled with the TALE toolbox following the published recommendations 37 . The plasmids for TALEN assembly were obtained from Addgene.…”

Section: Methodsmentioning

confidence: 99%

Efficient genome engineering by targeted homologous recombination in mouse embryos using transcription activator-like effector nucleases

et al. 2014

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Generation of mouse models by introducing transgenes using homologous recombination is critical for understanding fundamental biology and pathology of human diseases. Here we investigate whether artificial transcription activator-like effector nucleases (TALENs)-powerful tools that induce DNA double-strand breaks at specific genomic locations-can be combined with a targeting vector to induce homologous recombination for the introduction of a transgene in embryonic stem cells and fertilized murine oocytes. We describe the generation of a conditional mouse model using TALENs, which introduce double-strand breaks at the genomic locus of the special AT-rich sequence-binding protein-1 in combination with a large 14.4 kb targeting template vector. We report successful germline transmission of this allele and demonstrate its recombination in primary cells in the presence of Cre-recombinase. These results suggest that TALEN-assisted induction of DNA double-strand breaks can facilitate homologous recombination of complex targeting constructs directly in oocytes.

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“…A slower dissociation rate is necessary for the consensus site to increase TF dwell-time at the target location. These parameters can be considered guidelines for engineering novel transcription factors (63,64). Our data may also help guide and implement computational models of transcriptional regulation.…”

Section: Discussionmentioning

confidence: 99%

Massively parallel measurements of molecular interaction kinetics on a microfluidic platform

Geertz

Shore

Maerkl

2012

Proc. Natl. Acad. Sci. U.S.A.

103

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Quantitative biology requires quantitative data. No high-throughput technologies exist capable of obtaining several hundred independent kinetic binding measurements in a single experiment. We present an integrated microfluidic device (k-MITOMI) for the simultaneous kinetic characterization of 768 biomolecular interactions. We applied k-MITOMI to the kinetic analysis of transcription factor (TF)-DNA interactions, measuring the detailed kinetic landscapes of the mouse TF Zif268, and the yeast TFs Tye7p, Yox1p, and Tbf1p. We demonstrated the integrated nature of k-MITOMI by expressing, purifying, and characterizing 27 additional yeast transcription factors in parallel on a single device. Overall, we obtained 2,388 association and dissociation curves of 223 unique molecular interactions with equilibrium dissociation constants ranging from 2 × 10 −6 M to 2 × 10 −9 M, and dissociation rate constants of approximately 6 s −1 to 8.5 × 10 −3 s −1 . Association rate constants were uniform across 3 TF families, ranging from 3.7 × 10 6 M −1 s −1 to 9.6 × 10 7 M −1 s −1 , and are well below the diffusion limit. We expect that k-MITOMI will contribute to our quantitative understanding of biological systems and accelerate the development and characterization of engineered systems.biochemistry | biophysics | systems biology S ystems and synthetic biology, as well as the computational models and engineering-based approaches they employ, rely heavily on quantitative data (1, 2). Thus far, efforts in systems biology have mainly focused on cataloging and mapping genomes and proteomes. Genome sequencing and gene expression analysis have provided insight into genome architecture (3-6), and functional genomics approaches, including high-throughput protein-based methods (7-15), mapped network topologies.Although the number of known protein-protein and protein-DNA interactions is already substantial, the information describing such networks is predominantly qualitative and binary in nature. It is also becoming clear that network topologies alone are not sufficient to model complex biological processes. Precise quantitative information describing every interaction in a network would be tremendously valuable (2), yet binding affinities are known for only a small fraction of interactions (16, 17) and kinetic information hardly exists at all. This dearth of quantitative interaction data is due to a lack of high-throughput technologies capable of measuring kinetic rates of biomolecular interactions. Current methods used for kinetic rate measurements are generally based on surface plasmon resonance (SPR) (18) such as BioRad's ProteOn XPR36 6 × 6 array system, which measures 36 interactions in a single run. SPR-based measurements have been integrated with microfluidic devices (19, 20) to achieve higher degrees of parallelization (21). Yet proof of concept demonstrations have made use of only a small fraction of the proposed throughput and often restrict their measurements to protein-antibody interactions with high affinities and long half-lives...

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A transcription activator-like effector toolbox for genome engineering

Cited by 592 publications

References 60 publications

Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors

Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors

Efficient genome engineering by targeted homologous recombination in mouse embryos using transcription activator-like effector nucleases

Massively parallel measurements of molecular interaction kinetics on a microfluidic platform

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